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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgactattctgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA

Basic information

species Oryza sativa
transcript LOC_Os12g01580.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G150557_T01 (Zea mays), 3'ss of exon 6
gtaatgac-tattc------tgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
||||  || |  |       |||||| |  | |||| ||||   |||  || | ||  | ||| ||  | |     || |||||||||||||||||||||| ||||||| ||  | |||||| |||| ||||||                                                      
gtaagaacgtgcttgaaaaatgagaattttacacttaatttctgaagacatgtacagagattt-atgttcac-aattgttggatttttgcagTTTGTCACTATTTCTCAGCCGGTGAATGCTATTGCATTTGTGG-----------------------------------------------------

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM5G890665_T02 (Zea mays), 3'ss of exon 9
gtaatgac-tattc------tgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
||||  || |  ||      ||||||||    | || ||||   |||  || | ||  | ||| || ||     | || |||| ||||||||||||||||  ||||||| ||  | |||||| |||| || |||   |||||||||||||||||||||||||||||||| |  |  ||||| || || 
gtaagaacatgctccagaaatgagaagtttgcagttaatttctgaagaaatgtacagagattt-at-gttcccagttgttggacttttgcagTTTGTCACCATTTCTCAGCCGGTGAATGCTATTGCATTCGTGGCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACG

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G150557_T01 (Zea mays), 3'ss of exon 7
gtaatgactattctgagaagtcaatacttgatttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATG--GATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
                   |     | |     ||  ||| | | | |  |  |||  ||        |  ||  |    ||    |||   | | | |    | | ||   |   ||| ||| ||  ||  |||||||||||||||||||||||||||||||| |  |  ||||| || || 
-------------------gcttgcaat--gcatattaagcgttgtccgctaatttctta-----caacgcataaaaccatgtg--ttgctgcggatgcgttgcta-taggggtgtttgtgtt-gtagtgCTGATGGGCTCTACTATGGTGTTTCTGACTTTGCCTATGCTGCATATTCCACG

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G38330.1 (Arabidopsis thaliana), 3'ss of exon 10
gtaatgactattctgagaagtcaatacttgatttaccaag-tgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
||||   ||  |||   ||  ||  |   | || |  | | |  | |   |   | |   | ||||     | ||| |   ||||||||||  |||  ||||||||  | |||||| | ||||||||  ||||||||||||| |||||||| |||||||| |  || |  || || ||||  
gtaagatcttatcttttaatccagaaagagtttgaaaagggtagtctcagacaatatctaaataat-----gttggctggatgcagTTTGTGGCTGGATCTCAACCGGTGAATGCTCTAGCGTTTGTTTTGGATGGGCTCTATTATGGTGTCTCTGACTTCGGATTTGCCGCTTATTCTATG

upper sequence: LOC_Os12g01580.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv08s0058g00510.t01 (Vitis vinifera), 3'ss of exon 10
--------gtaatgactattctgagaagtcaata------cttgatttaccaagtg-atatgcaatggttttatagtaattggc-tgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
        ||    | | |  ||   |||  |||      |||   | |    ||| ||  || |||   ||  || ||||    | ||  | |||||||||||||  |||  ||||||||||| |||||| |||| ||||| || ||||| ||||||||||| ||||| |||||||  |  |  || ||||| |  
gtttccatgtggc-attctattggtgagtgcataaactggcttacctcatttggtgcatgggctatgtcatttaagaaatttatgttataaaattttgcagTTTGTTGCTGGATCTCAACCAATGAATGCTATTGCATTTGTTATTGATGGACTCTACTATGGGGTTTCAGACTTTGGATATGCTGCCTACTCCATG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29639601|gb|CB644610.1|CB644610
EST:     TGTTTACAGATGATGCAGCAGTTTTAGACGTTGCCCAAACTGGAGTCTGG                         TTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGG
genomic: TGTTTACAGATGATGCAGCAGTTTTAGACGTTGCCCAAACTGGAGTCTGGgtaatgacta ... atttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGG
EST: gi|25806216|gb|CA762177.1|CA762177
EST:     GACGTTGCCCAAACTGGAGTTTGG                         TTNGTCCCTGTTTCTCAACCCATAAATGCTGTTGCGTTTGTGAAGGATGGG
genomic: GACGTTGCCCAAACTGGAGTCTGGgtaatgacta ... atttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 66 (upstream exon), 30 (downstream exon)
Score: 7

TGCAGCACTTTCTACAACCTTACTCCTTGGGTTTGGATATTTGTCCATGCTGTTTACAGATGATGCAGCAGTTTTAGACGTTGCCCAAACTGGAGTCTGGgtaatgacta ... atttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttaccaagtgatatgcaatggttttatagtaattggctgatggatttttgcagTTTGTCACTGTTTCTCAACCAATAAATGCTGTTGCGTTTGTGATGGATGGGCTCTACTATGGTGTTTCTGACTTTGCTTTCGTGGCATACTCTACA
                                    ggctgat  putative branch site (score: 7)
                                              tttttgc  putative PPT
                       ttttatagtaatt  TA-rich tract